Replace jnml in scripts with pynml?

[travs]

@gsarma and I have been running some things in this repo recently, but we couldn't get jNeuroML to install correctly. If we replaced calls to jnml with pynml they seemed to work fine and produce output.

There are only a few places where we would have to replace this.

@pgleeson Do you think the functionality in pyNeuroML is such that we can do this right now?

[cheelee]

I was previously able to build jnml using the jNeuroML repository instructions. It was a little clunky to use but it worked. Having said that, if it works with just pynml I'd suggest sticking to just one set of instructions initially for users.

[pgleeson]

I've made some more updates here: https://github.com/openworm/muscle_model/blob/master/NeuroML2/README.md.

If there are specific issues with the installation instructions of jnml, please add details https://github.com/NeuroML/jNeuroML/issues.

PyNeuroML is probably stable enough that the installation details from .travis.yml could be replaced in section 2.1 of the main README.